The nasty way to do it, to be avoided since it is theme pollution the merchant may not know how to clean.
- Download the merchants currently active theme.liquid, add your code, and re-upload the theme.liquid file with your changes.
The nice way to do it, since the script is automatically removed when your App is uninstalled.
- inject a script tag file that alters the theme dynamically to include your code.
Not a tough decision for you to make.